SPiPtainer

apptainer for SPiP

Pre-requisites

You need Apptainer up and running.

Build

apptainer build spiptainer.sif spiptainer.def

Run

You need an input file (see SPiP repo for specifications) and the trasncriptome reference file used by SPiP, then

apptainer run \
--bind /path/to/RefFiles:/RefFiles \
spiptainer.sif  \
-I /RefFiles/test_spip.txt \
-O /RefFiles/test_results.txt \
-g hg38 \
--transcriptome /RefFiles/transcriptome_hg38.RData